Adding a ref point support for atom selection

[abdulasiraj]

Fixes #4344

Changes made in this Pull Request:

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

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📚 Documentation preview 📚: https://mdanalysis--4348.org.readthedocs.build/en/4348/

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.23%. Comparing base (73acc9b) to head (1b7f3e9).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4348      +/-   ##
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- Coverage    93.66%   93.23%   -0.44%     
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  Files          168       12     -156     
  Lines        21248     1079   -20169     
  Branches      3917        0    -3917     
===========================================
- Hits         19902     1006   -18896     
+ Misses         888       73     -815     
+ Partials       458        0     -458     

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[richardjgowers]

This looks like a good start, this is trying to make refpoint x y z a possible selection as part of a command like sphlayer in the selection language.

The return from _apply here needs to usually be an AtomGroup, as other selections will expected it to provide things like center_of_geometry: https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/core/selection.py#L348

There's probably two ways to make this work:

1. you could make the _apply method here return a AtomGroup-like object, so define a PseudoAtomGroup class here that duck types (imitates) all the required methods (like center_of_geometry etc).
2. instead, make all geometric selections that require a selection, instead have a branch where they can instead parse the refpoint here. This would change the signature of sphlayer 1.0 2.0 selection OR refpoint

Option 2 here is probably more lines of code and seems less elegant, but option 1 seems a little fragile as the pseudo AtomGroup class would require a lot of maintenance to keep it behaving like a real AtomGroup

[orbeckst]

Thanks for the contribution @abdulasiraj and thanks for the initial round of feedback @richardjgowers .

As there's still a WIP-label in the title I assume that you still want to do a fair amount of work by yourself @abdulasiraj . Once you think it's really ready for review, please change the name and then we can have closer look.

[RMeli]

@abdulasiraj I removed the WIP label to the title and converted this PR into a draft, to avoid confusion. Please feel free to mark it as "Ready to review" when it's no longer WIP.

[abdulasiraj]

That's make more sense. I'll update for sure. Thanks @RMeli

[orbeckst]

@abdulasiraj are you still working on this PR? Otherwise we will close it.

[abdulasiraj]

Hi @orbeckst, I'll complete it in few days hopefully. just got time to work on it. Thanks!